Project Summary/Abstract: This application is being submitted for PA-18-591 in accordance with NOT-OD-18-194. The Birth Defects Research Laboratory (BDRL) is a fetal tissue repository with an over 50-year history of NIH-funding. The primary goal of BDRL is to systematically collect, stage, and distribute high-quality normal and abnormal conceptal tissues, including Down syndrome, and their biologics to university and non-profit affiliated investigators for biomedical research. This application proposes to develop the resource beyond its core goals by creating a Developmental Cell Atlas of Down syndrome for brain, bone marrow, heart, intestine, liver, lung, spleen, thymus and skin fibroblasts using single-cell transcriptomics. Down syndrome is the most prevalent genetic disorder in humans and a major cause of intellectual disability. Despite the discovery of the genetic cause of Down syndrome ~60 years ago, the details of the biological mechanisms leading from an extra copy of chromosome 21 to intellectual disability and the many other associated conditions (Alzheimer disease, structural heart defects, leukemia, intestinal abnormalities, and autoimmune disorders) remain unknown. BDRL is uniquely positioned to generate a map of the cellular landscape of Down syndrome to understand how trisomy 21 leads to alterations in development and function. We directly address Components 1 and 2 of the INCLUDE project by creating a single-cell atlas to molecularly define 9 fetal tissues affected by important clinical features in Down syndrome, using affected tissues banked in our repository. Creating this atlas for Down syndrome will allow direct comparisons to a developmental reference cell atlas generated using the same methods. The samples remaining from the atlas will constitute a well-characterized cell and tissue repository for Down syndrome available to investigators for additional experiments. The Developmental Cell Atlas for Down Syndrome will provide unprecedented developmental phenotyping of Down syndrome at single cell resolution, which will set the stage for future hypothesis-driven experiments to develop targeted treatments.